Putting an embryo back together – cell by cell

Patterned gene expression drives early development as cells specify and differentiate. We disassembled early embryos at the onset of gastrulation into single cells and sequenced the transcriptomes of thousands of individual cells. Center: The sequenced cells cluster according to transcriptome similarity as represented by tSNE; each cluster distinguishes itself by combinatorial expression of characteristic genes. Periphery: To reveal the spatial information hidden in the transcriptomes of individual cells, we developed mapping algorithms to accurately place cells back onto a map of the embryo. Lateral views of virtual embryos show the location of cluster cells.

Not shown is that once cells are mapped, the resulting virtual embryo lets us predict the expression across thousands of coding and non-coding transcripts at the single cell level (virtual in situ hybridizations). This, in turn, allows novel insights into where and in what combinations genes are expressed, how nearby cells communicate, and how spatial gene expression patterns evolve among related drosophilids.